Effects Of Genetic Variants Research Articles

EvoDevo Shapes the Extended Synthesis

When the interfield of EvoDevo arose in the early 1980s, its momentum was fueled by both the methodological advances in molecular biology and the explanatory deficits of the standard evolutionary paradigm, the Modern Synthesis. Whereas the methodological progress led to a proliferation of empirical research, the implications of EvoDevo for evolutionary theory often went unnoticed or were actively sidelined by the stakeholders of the received theory. Only with the progressive corrosion of the Synthesis framework due to challenging evidence from several more fields (genomics, epigenetics, physiology, behavior, etc.) the tide started to change, and EvoDevo has become one of the key players in the current redefinition of evolutionary theory. The evidence produced by EvoDevo mostly bears on the complexity of the genotype–phenotype rapport and the gene regulatory changes underlying its evolutionary transformation. It also elucidates the cell and tissue properties involved in the generation of complex structures, the physics and physiology governing these processes, as well as the quantitative assessment and modeling of generative procedures in evolutionary contexts. These results have tremendously improved our understanding of how development originated in the context of multicellularity, how its repertoires evolved, and how organismal change is mechanistically realized. EvoDevo has been equally prolific in the conceptual domain, contributing a wealth of new principles to the evolutionary model. Besides elaborations of such classical issues as heterochrony and developmental constraint, EvoDevo gave rise to new concepts such as facilitated variation, developmental modularity, morphoregulation, epigenetic innovation, developmental systems drift—to name but a few. These provided improved understanding of the evolvability of developmental systems and their contribution to evolutionary robustness and non-gradual phenomena of phenotypic change. The result of these endeavors was a broadened interpretation of the role of development in the evolution of organismal complexity. Today it can be concluded with much confidence that the generation of selectable variation and phenotypic structure is not merely a consequence of genetic variation but also of the capacity of plastic developmental systems to respond to natural selection and direct environmental induction with integrated and often emergent reactions. Development not only constrains and facilitates the generation of phenotypic variation, but also affects the tempo, mode, and directionality of evolutionary change. In concert with the evidence emerging from other fields of evolutionary biology, as briefly mentioned above, the findings of EvoDevo mean that nearly all assumptions central to the traditional Modern Synthesis framework have been overturned: evolution is not just a variational, continuous, and incremental kind of change but involves alternating speeds and discontinuous events; not all organismal features are independently adaptive, but certain traits are emergent and evolutionarily neutral; phenotypic variation is not merely a product of genetic variation that arises randomly and at constant rates but is equally a product of integrated development and plasticity; no single Gerd Muller is president of the European Society for Evolutionary Developmental Biology.

Progress in Pharmacogenomics: Bridging the Gap From Research to Practice

Genetic information is increasingly used to optimize clinical treatment of patients, but obstacles remain to practical implementation as well as challenges to our understanding of genetic variation in drug response. These areas that particularly require research attention include gene-environment interactions, the consequences of genetic variation, and the impact of epigenetics on gene expression and function. In this issue of Clinical Pharmacology & Therapeutics focused on pharmacogenetics, we discuss some of the recent advances in understanding from a variety of viewpoints.

Genetic and epigenetic variation in mass selection populations of Pacific oyster Crassostrea gigas

Selective breeding often produces an improvement in phenotype. Much of the phenotypic change within a species is a consequence of genetic variation. However, there is growing evidence for phenotypic change even in the absence of DNA sequence polymorphisms, termed epigenetic variation. This study’s goal was to investigate the genetic and epigenetic variation in the mass selection populations of the Pacific oyster (Crassostrea gigas), determine if any correlation exists between the genetic and epigenetic variations. This can serve as a first step in investigating the potential role epigenetic variations have in selective breeding. Amplified fragment length polymorphism analysis and methylation-sensitive amplified polymorphism methodology were used to monitor genetic and epigenetic variation in two populations (the base stock and the third selected generation) from a mass selection line in the Pacific oyster. The correlation between genetic and epigenetic variation was evaluated by Co-Inertia Analysis. The genetic difference was mainly found in the gene frequency shift revealed by the FST value (0.0151, P < 0.01) and no significant reduction in genetic diversity was detected. The percentage of methylation in C. gigas was 26.4 %. No significant difference was observed on the average state of methylation, but a few bands showed different frequencies between the two populations. Co-Inertia Analysis revealed a significant association between the genetic and epigenetic profiles (P < 0.01).

P.3.a.014 Exploring the effect of genetic variability of adducins on cognition in schizophrenia

P.3.a.014 Exploring the effect of genetic variability of adducins on cognition in schizophrenia

The consequences of genetic variation in sex peptide expression levels for egg laying and retention in females

The accessory gland proteins (Acps) that male Drosophila melanogaster produce and transfer to females during copulation are key to male and female fitness. One Acp, the sex peptide (SP), is largely responsible for a dramatic increase in female egg laying and decrease in female receptivity after copulation. While genetic variation in male SP expression levels correlate with refractory period duration in females, it is unknown whether male SP expression influences female egg laying or if any effect of SP is mediated by SP retention in the female reproductive tract. Here we measured the amount of SP retained in the female reproductive tract after mating and female egg laying after copulating with virgin males. We found no correlation between male SP expression levels and egg laying, or the amount of SP in the female reproductive tract after mating. Additionally, the amount of SP retained in the female did not influence egg laying. These finding suggests that additional factors, such as variation in other Acps, are important for the retention of SP in females and its quantitative effects on egg laying. It also shows that egg laying and refractory period response to SP is at least partially uncoupled.

Genetic Variability in 8q24 Confers Susceptibility to Urothelial Carcinoma of the Upper Urinary Tract and is Linked With Patterns of Disease Aggressiveness at Diagnosis

Upper urinary tract urothelial carcinoma is rare. Evidence shows that it behaves differently from urothelial bladder tumors. A polymorphism located at the T allele of rs9642880 on chromosome 8q24 is linked to an enhanced risk of bladder tumors. We explored the association of this polymorphism with susceptibility to upper urinary tract urothelial carcinoma. We genotyped the constitutional DNA of 261 patients with upper urinary tract urothelial carcinoma and 261 healthy controls matched for age, gender, smoking habit and ethnicity. Polymorphisms at rs9642880 on chromosome 8q24 were determined using the 5' nuclease polymerase chain reaction method with specific primers and probes. Frequencies were compared between cases and controls. Genotypes were in Hardy-Weinberg equilibrium for cases and controls. Mean patient age was 68.7 years. The T/T genotype resulted in a significantly higher risk of upper urinary tract urothelial carcinoma (OR 1.72, 95% CI 1.1-2.8, p = 0.028). Using single polytomous regression analysis the T/T genotype was also associated with aggressive tumors when stratified by stage (p = 0.003), or grade G2 (p = 0.04) or G3 (p = 0.01). Our results strongly suggest that the T/T rs9642880 genotype is a risk factor for upper urinary tract urothelial carcinoma, as previously shown for bladder tumors. In contrast to bladder carcinoma, for upper urinary tract urothelial carcinoma the T/T genotype is associated with aggressiveness.

Adiponectin Level as a Consequence of Genetic Variation, but Not Leptin Level or Leptin

The adipocytokines adiponectin and leptin have been suggested as risk factors for cardiovascular disease, including stroke, acting through atherosclerosis. However, studies have provided conflicting results in underpowered cohorts with some suggesting that the leptin:adiponectin ratio is a better predictor of risk. We examined these associations with carotid intima-media thickness (IMT), a marker of early atherosclerosis and arterial remodeling and an independent predictor of stroke. We also examined association between genetic variants in the leptin and adiponectin genes and IMT. Adiponectin and leptin levels were determined in 990 individuals from the community Carotid Atherosclerosis Progression Study. Five variants in the gene encoding adiponectin and 7 in the gene encoding leptin were genotyped and their effects on circulating levels assessed. Both were then correlated with IMT. Adiponectin levels negatively correlated with IMT (-0.079, P=0.013). There was no correlation between leptin levels or leptin:adiponectin ratio and IMT. Two variants in the ADIPOQ gene encoding adiponectin were associated with altered adiponectin levels, 1 of which (rs266729) was associated with IMT. There was also an interaction with body mass index (P=0.019) with the association being present in obese subjects (P=0.02). Our results support a causal role for adiponectin in early carotid IMT and suggest it may act through interaction with obesity. In contrast, we found no evidence of a role for leptin and no evidence that leptin:adiponectin ratio is a better predictor of risk that adiponectin levels alone.

Effects of genetic variability of the dairy goat growth hormone releasing hormone receptor (GHRHR) gene on growth traits

Growth hormone-releasing hormone receptor (GHRHR) plays a critical role in growth hormone (GH) synthesis, release and regulation of pituitary somatotroph expansion in vertebrates. The objective of this study was to investigate variations in goat GHRHR gene and their associations with growth traits in 668 dairy goats. The results showed four novel single nucleotide polymorphisms (SNPs): NC_007302:g.5203C>T, 7307C>G, 9583G>A and 9668A>C. In detail, the novel SNP C>T in the 5203rd nucleotide identified a missense mutation: CCC (Pro)>TCC (Phe) at position 116aa of the goat GHRHR (423aa). Besides, 9583G>A and 9668A>C polymorphism were in complete linkage disequilibrium. The genetic diversity analysis revealed that the Guanzhong dairy goat possessed intermediate genetic diversity in P3 and P7 loci, and the Xinong Sannen dairy goat belonged to poor genetic diversity in P4 locus. Significant associations between the genotypes of P3 locus and body length, body height and chest circumference was observed in Guanzhong goat (P<0.05). However, in Xinong saanen population, significant statistical difference was only found in body height and body length (P<0.05). In P4 and P7 loci, no significant associations were detected between any variant sites and body length, body height and chest circumference, as well as for the milk traits (P>0.05). These results strongly suggested that the goat GHRHR gene is a candidate gene that influences growth traits in dairy goat.

Genetic selection? A study of individual variation in the enzymes of folate metabolism

BackgroundGenetic variation in folate metabolism has been associated with survival in utero, the success of in vitro fertilisation, multiple pathologies and longevity.MethodsWe have looked at the prevalence of genetic variants of the enzymes MTHFR and TYMS in 2,898 DNA samples derived from five cohorts collected in the United Kingdom. The simultaneous analysis of genetic variants of the MTHFR and TYMS loci was carried out to investigate a putative gene-gene interaction that was first observed in an elderly male population from Norfolk.ResultsWe have made a consistent observation in five population cohorts; the proportion of individuals who are homozygous for the 2R allele of the 5'UTR TYMS polymorphism is less in individuals who are homozygous for the T allele of MTHFR 677 than in individuals homozygous for the C allele of MTHFR 677 (p = 0.02).ConclusionsThese data may suggest a gene-gene interaction and could be evidence of genetic selection, with some pregnancies more or less viable as a consequence of genetic variation. If these genetic phenomena affect the way folate is handled at the cellular level in utero it is possible that maternal folic acid intake may over-ride such genetic selection.

Le diabète et l’obésité, réellement des maladies héritées d’un passé de chasseurs-cueilleurs ?

According to the thrifty genotype hypothesis, the high prevalence of type 2 diabetes and obesity is a consequence of genetic variants that have undergone positive selection during historical periods of erratic food supply. The recent expansion in the number of validated type 2 diabetes- and obesity-susceptibility loci, coupled with access to empirical data, enables us to look for evidence in support (or otherwise) of the thrifty genotype hypothesis using proven loci. We employed a range of tests to obtain complementary views of the evidence for selection: we determined whether the risk allele at associated “index” sing-lenucleotide polymorphisms is derived or ancestral, calculated the integrated haplotype score (iHS) and assessed the population differentiation statistic fixation index (FST) for 17 type 2 diabetes and 13 obesity loci. We found no evidence for significant differences for the derived-ancestral allele test. None of the studied loci showed strong evidence for selection based on the iHS score. We find a high FST for rs7901695 at TCF7L2, the largest type 2 diabetes effect size found to date. Our results provide some evidence for selection at specific loci, but there are no consistent patterns of selection that provide conclusive confirmation of the thrifty genotype hypothesis. Discovery of more signals and more causal variants for type 2 diabetes and obesity is likely to allow more detailed examination of these issues.

Effect of human immunodeficiency virus type 1 protease inhibitor therapy and subtype on development of resistance in subtypes B and G

Europe is currently observing a significant rise in non-B subtypes. Consequently, the effect of genetic variability on therapy response or genotypic resistance interpretation algorithms is an emerging concern. The purpose of this study is to investigate the amino acid substitutions selected under drug pressure in the protease of human immunodeficiency virus type 1 (HIV-1) subtypes B and G, and determine if there are any significant differences. We investigated therapy-related and subtype-related substitutions in the protease, considering subtype, overall protease inhibitor treatment and individual drug exposure. Many mutations were significantly related to protease inhibitor (PI) therapy, with mutations exclusive to subtype B or subtype G. Some mutations are at positions related to resistance in both subtypes, but the amino acid substitution is different. Other mutations were significantly associated with subtype and PI selective pressure ( p < 0.05), pointing towards a differential selective pressure in both subtypes. We confirmed previous reports on the subtype-dependent selection of D30N and 89I, and identified a new mutation with such differential selective pressure: 37D was preferentially selected by lopinavir in subtype B. Other novel mutations found under therapy pressure were 13A, 35N, K55R, I66F, I72L/T, T74S, 82M and 89I/V. Our study indicates that even though in general, drug selective pressure and resistance pathways are relatively similar between subtypes B and G, some differences do occur, leading to subtype-dependent substitutions.

Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?

Aims/hypothesisAccording to the thrifty genotype hypothesis, the high prevalence of type 2 diabetes and obesity is a consequence of genetic variants that have undergone positive selection during historical periods of erratic food supply. The recent expansion in the number of validated type 2 diabetes- and obesity-susceptibility loci, coupled with access to empirical data, enables us to look for evidence in support (or otherwise) of the thrifty genotype hypothesis using proven loci.MethodsWe employed a range of tests to obtain complementary views of the evidence for selection: we determined whether the risk allele at associated ‘index’ single-nucleotide polymorphisms is derived or ancestral, calculated the integrated haplotype score (iHS) and assessed the population differentiation statistic fixation index (FST) for 17 type 2 diabetes and 13 obesity loci.ResultsWe found no evidence for significant differences for the derived/ancestral allele test. None of the studied loci showed strong evidence for selection based on the iHS score. We find a high FST for rs7901695 at TCF7L2, the largest type 2 diabetes effect size found to date.Conclusions/interpretationOur results provide some evidence for selection at specific loci, but there are no consistent patterns of selection that provide conclusive confirmation of the thrifty genotype hypothesis. Discovery of more signals and more causal variants for type 2 diabetes and obesity is likely to allow more detailed examination of these issues.

The human Major Histocompatibility Complex as a paradigm in genomics research

Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became the first genomic region to be entirely re-sequenced for common haplotypes, while studies mapping gene expression phenotypes across the genome have strongly implicated variation in the MHC. This review shows how the MHC continues to provide new insights and remains in the vanguard of contemporary research in human genomics.

Counterpoint: Estrogen and Sex do not Significantly Influence Post-Exercise Indexes of Muscle Damage, Inflammation, and Repair

Exercise-induced muscle damage (EIMD) occurs following strenuous, novel exercise and is assessed directly via tissue analysis and characterized indirectly by muscle dysfunction, inflammation, delayed onset muscle soreness, and increased levels of muscle proteins [e.g., creatine kinase (CK),

The clinical impact of pharmacogenetics on the treatment of epilepsy

Drug treatment of epilepsy is characterized by unpredictability of efficacy, adverse drug reactions, and optimal doses in individual patients, which, at least in part, is a consequence of genetic variation. Since genetic variability in drug metabolism was reported to affect the treatment with phenytoin more than 25 years ago, the ultimate goal of pharmacogenetics is to use the genetic makeup of an individual to predict drug response and efficacy, as well as potential adverse drug events. However, determining the practical relevance of pharmacogenetic variants remains difficult, in part because of problems with study design and replication. This article reviews the published work with particular emphasis on pharmacogenetic alterations that may affect efficacy, tolerability, and safety of antiepileptic drugs (AEDs), including variation in genes encoding drug target (SCN1A), drug transport (ABCB1), drug metabolizing (CYP2C9, CYP2C19), and human leucocyte antigen (HLA) proteins. Although the current studies associating particular genes and their variants with seizure control or adverse events have inherent weaknesses and have not provided unifying conclusions, several results, for example that Asian patients with a particular HLA allele, HLA-B*1502, are at a higher risk for Stevens-Johnson syndrome when using carbamazepine, are helpful to increase our knowledge how genetic variation affects the treatment of epilepsy. Although genetic testing raises ethical and social issues, a better understanding of the genetic influences on epilepsy outcome is key to developing the much needed new therapeutic strategies for individuals with epilepsy.

Effect of Genetic Variability within 8q24 on Aggressiveness Patterns at Diagnosis and Familial Status of Prostate Cancer

Recently, two independent loci located at 8q24 that contribute to prostate cancer risk in men of European origin were identified. Using Bayesian probability network and logistic regression model, we searched for associations between 34 single-nucleotide polymorphisms (SNP) located at 8q24 and the aggressiveness patterns of prostate adenocarcinoma or familial history of cancers in 823 White Caucasian French men. Probability network according to the Markov chain algorithm separated the SNPs into two main groups: The first one was linked to the locus marked by rs6983267 and the second one was linked to the locus marked by rs1447295. When the patients were stratified according to tumor stage and prostate-specific antigen value, the association between the variant genotypes from six SNPs located in the second network and prostate cancer risk was strongest or confined to the patients from the more aggressive classes. However, the association between prostate cancer risk and the CC genotype of rs7841264, which marked the recombination hotspot at 8q24, was confined to patients with the highest Gleason score (odds ratio, 2.15; 95% confidence interval, 1.27-3.64; P=0.004). Interestingly, the G allele of rs6983267 was associated with familial prostate cancer risk. Our data further support that variability at 8q24 is associated with a high risk of aggressive prostate cancer at diagnosis and is linked with familial history of prostate cancer. These results corroborate that 8q24 SNPs must be evaluated in terms of prostate cancer aggressiveness markers to optimize early diagnosis procedures and management of the disease.

Effects of genetic variability, parts and seasons on the sterol content and composition in bamboo shoots

Bamboo shoots are regarded as potential sources of sterols. The effects of genetic variability, parts and harvest seasons on the sterol content and composition in the bamboo shoots have been determined using a novel ultra-performance liquid chromatographic atmospheric pressure chemical ionisation mass spectrometer method. The results showed that the representative sterols in bamboo shoots were β-sitosterol, campesterol, stigmasterol, ergosterol, cholesterol and stigmastanol; exception stigmastanol, the significant differences were observed in the sterol content of different species (112.4–279.6 mg/100 g dry wt), different harvest seasons (195.3–279.6 mg/100 g dry wt) and different parts (253.6–321.8 mg/100 g dry wt); the sterol composition was similar in different species and different harvest seasons, however, it was significantly different between shoot bodies and shoot shell. The genetic variability, parts and harvest seasons could significantly affect the sterol composition in the bamboo shoots. The spring shoot shell of Phyllostachys pubescens contained the highest sterol content (321.8 mg/100 g dry wt).

Thyroid Hormone Transport and Metabolism by Organic Anion Transporter 1C1 and Consequences of Genetic Variation

Organic anion transporting polypeptide (OATP) 1C1 has been characterized as a specific thyroid hormone transporter. Based on its expression in capillaries in different brain regions, OATP1C1 is thought to play a key role in transporting thyroid hormone across the blood-brain barrier. For this reason, we studied the specificity of iodothyronine transport by OATP1C1 in detail by analysis of thyroid hormone uptake in OATP1C1-transfected COS1 cells. Furthermore, we examined whether OATP1C1 is rate limiting in subsequent thyroid hormone metabolism in cells cotransfected with deiodinases. We also studied the effect of genetic variation in the OATP1C1 gene: polymorphisms were determined in 155 blood donors and 1192 Danish twins and related to serum thyroid hormone levels. In vitro effects of the polymorphisms were analyzed in cells transfected with the variants. Cells transfected with OATP1C1 showed increased transport of T4 and T4 sulfate (T4S), little transport of rT3, and no transport of T3 or T3 sulphate, compared with mock transfected cells. Metabolism of T4, T4S, and rT3 by cotransfected deiodinases was greatly augmented in the presence of OATP1C1. The OATP1C1-intron3C>T, Pro143Thr, and C3035T polymorphisms were not consistently associated with thyroid hormone levels, nor did they affect transport function in vitro. In conclusion, OATP1C1 mediates transport of T4, T4S, and rT3 and increases the access of these substrates to the intracellular active sites of the deiodinases. No effect of genetic variation on the function of OATP1C1 was observed.

The functional consequences of genetic variations in transporter genes encoding human organic anion-transporting polypeptide family members

It is increasingly recognised that uptake transporters of the organic anion-transporting polypeptide (OATP) family play important roles in drug absorption, distribution and excretion. They are expressed in a variety of different tissues, including gut, brain, kidney and liver. Substrates of OATPs include several endogenous substances, such as bile salts and hormones, and drugs such as HMG-CoA reductase inhibitors (e.g., pravastatin), cytotoxic drugs and antibiotics. Recent advances in the pharmacogenetics of OATPs have demonstrated that variations (polymorphisms) in genes encoding human OATPs can explain parts of the interindividual variability in the pharmacokinetics of drugs and, thus, contribute to the interethnic and interindividual variability in drug response. This review focuses on consequences of these genetic variations and summarises in vivo as well as in vitro analyses demonstrating the impact of polymorphisms in genes encoding OATPs on transport and pharmacokinetics of drugs.

Identification Genetic Variations (GVs) Causing Splicing of TNF Family Members and Adaptor Proteins That Modulate NFkB Pathways in Waldenstrom's Maroglobulinemia (WM).

The TNF ligand-receptor superfamily and their adaptor proteins regulate important B-cell signaling pathways, including CD40L-CD40 and APRIL/BLYS-TACI through adaptor protein TRAF2. These pathways promote B-cell differentiation and immunoglobulin heavy chain class switching. Defects in immunoglobulin heavy chain class switching and presence of constitutive IgA and IgG hypogammaglobulinemia in patients with WM have previously been reported by us (Hunter et al, ASH2006). In WM patients we identified several novel splice variants of TNF-family members CD40 and BLYS, and their adaptor protein TRAF2. Cloning, sequencing and alignment analysis document that aberrant splice transcripts of CD40, CD40-Va, Vb and Vc, and BLYS, BLYS-Va and Vb, result from partial exon skipping (CD40Va and Vc) and entire or partial intron retention (CD40-Vb, BLYS-Va and Vb), while the TRAF2 variant is a result of exon skipping only. Using RT-PCR DNA fragment analysis, malignant and normal B-cells from the bone marrow of 25 WM patients and 6 healthy donors (HDs) were screened for the expression of CD40, BLYS and TRAF2 splice transcripts. This analysis identified overexpression of CD40-Vb (15/25WM vs. 0/6HD; P=0.01), CD40-Vc (21/25WM vs. 0/6HD; P=0.0003), BLYS-Vb (18/25WM vs. 0/6HD; P=0.002) and TRAF2-V (21/25WM vs. 1/6HD; P=0.004) in WM patients. The expression of other splice variants CD40-Va (18/25WM vs.2/4HD; P=0.09) and BLYS-Va (23/25WM vs. 4/6HD P=0.2) in the same group of WM patients were not significant. We hypothesized that these aberrations are consequences of genetic variations (GVs) distributed in the vicinity of splicing elements of these genes, as well as, alterations may have occurred in the repertoire of splicing factors (SFs) with respect of their expression levels. To address these issues, we started sequencing CD40, BLYS, and TRAF2 gene segments that are subjected to aberrant splicing. Sequencing analysis of the CD40 gene from WM B cells revealed 6 recurrent genetic variations (GVs-defined as mutations occurring more than one patients) that include 2 missense (on exon 3) and 3 silent substitutions (on exons 3-4-5), and 1 frame-shift deletion on exon 5. These substitutions lead to amino acid changes on CD40 gene, while the frame-shift deletion may cause truncation of wild-type CD40 protein. We also identified recurrent GVs on introns 4 and 5. All these GVs detected on exons and introns are distributed in the vicinity of key splicing elements that create and/or activate a new splice site in precisely the position required for the splicing events to create CD40 variants. Also, using TaqMan low density array (TaqMan-LDA) we evaluated levels of major SFs and other TNF family members involved in CD40 and BLYS signaling. These analyses showed that patients expressing aberrant splice variants of CD40 and BLYS overexpress not only other members of TNF family but also major SFs: SF2/ASF (a proto-oncogene), U2, hNRPA1 and SRP55. TaqMan-LDA analysis suggests that these SFs may play a significant role in CD40, BLYS and TRAF2 splicing in WM patients since these transcripts were upregulated (1.2-2.2 fold higher) only in those patients which expressed CD40, BLYS and TRAF2 variants. In conclusion, presence of GVs in the vicinity of splicing elements and upregulation of SFs collectively may promote aberrant CD40, BLYS and TRAF2 splicing and thus modulate TNF family pathways supportive of B-cell differentiation and immunoglobulin heavy chain class switching in patients with WM.